Activation fingerprints and allosteric modulation at the free fatty acid receptor 1 (FFAR1) revealed by molecular dynamics simulation

The free fatty acid receptor 1 (FFAR1) is a transmembrane G-protein coupled receptor that mediates the metabolic and insulinotropic effects of endogenous free fatty acids in pancreatic cells while also exerting neuro-regulatory effects in the brain. The complexity of FFAR1 derives from its multiple binding sites and the absence of conventional activation motifs observed in class A GPCRs. This study uses molecular dynamics simulations to investigate the molecular mechanisms that underpin endogenous signaling and allosteric regulation in the FFAR1. We investigated and compared three ligand-bound states and the APO state. The ligand-bound simulations included FFAR1 in complex with γ-linolenic acid, FFAR1 in complex with γ-linolenic acid and TAK875, and a fully activated FFAR1 bundle complexed with docosahexaenoic acid and G-protein. The results highlight distinct protein contact fingerprints and dynamics in the ligand-bound states relative to the APO state. While ligand binding, in the absence of stabilizing G-protein, destabilizes the intracellular domain of the receptor, the second extracellular loop exhibits greater stability and salt bridge contact with the transmembrane domain. Notably, simulations of FFAR1 complexed with γ-linolenic acid, bound at the intracellular domain, revealed stable interactions between γ-linolenic acid and the receptor, as well as similar activation fingerprints when compared to FFAR1 in complex with docosahexaenoic acid and Gq. This suggests an effective allosteric regulation of the receptor following γ-linolenic acid binding to the intracellular domain. Finally, a set of hydrophobic amino acid residues at the intracellular and extracellular domains appears to function as potential rotameric switches, facilitating water-mediated receptor activation.